Package: cheddar 0.1-639

cheddar: Analysis and Visualisation of Ecological Communities

Provides a flexible, extendable representation of an ecological community and a range of functions for analysis and visualisation, focusing on food web, body mass and numerical abundance data. Allows inter-web comparisons such as examining changes in community structure over environmental, temporal or spatial gradients.

Authors:Lawrence Hudson with contributions from Dan Reuman and Rob Emerson

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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
cheddar/json (API)

# Install 'cheddar' in R:
install.packages('cheddar', repos = c('https://quicklizard99.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/quicklizard99/cheddar/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

Conda:

cpp

6.90 score 19 stars 168 scripts 413 downloads 1 mentions 199 exports 0 dependencies

Last updated from:c2fea5ff5b. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK144
linux-devel-x86_64OK142
source / vignettesOK170
linux-release-arm64OK132
linux-release-x86_64OK130
macos-release-arm64OK125
macos-release-x86_64OK231
macos-oldrel-arm64OK89
macos-oldrel-x86_64OK344
windows-develOK122
windows-releaseOK125
windows-oldrelOK119
wasm-releaseOK93

Exports:[.CommunityCollection[[<-.Community[[<-.CommunityCollection[<-.Community[<-.CommunityCollection$<-.Community$<-.CommunityCollectionAggregateCommunitiesAggregateCommunitiesByApplyByClassBasalNodesBiomassBodyMassBinsCannibalsChainAveragedTrophicLevelCharacteristicPathLengthCollectionApplyCollectionCPSCollectionNPSCollectionTLPSCommunityCommunityCollectionCommunityPropertyNamesConnectedNodesConsumersByNodeConsumersOfNodesCPCPSCRMRatioDefaultCategoryColoursDefaultCategoryLabelColoursDefaultCategorySymbolsDefaultLinkColourDegreeDegreeDistributiondim<-.Communitydim<-.CommunityCollectionDirectedConnectanceFlowBasedTrophicLevelFormatLMFractionBasalNodesFractionCannibalisticFractionConnectedNodesFractionIntermediateNodesFractionIsolatedNodesFractionNonBasalNodesFractionNonTopLevelNodesFractionOfNodesByClassFractionOmnivorousFractionTopLevelNodesHasMHasNHasTrophicLinksInDegreeIntermediateNodesis.Communityis.CommunityCollectionIsBasalNodeIsCannibalIsConnectedNodeIsIntermediateNodeIsIsolatedNodeIsNonBasalNodeIsNonTopLevelNodeIsolatedNodesIsOmnivoreIsTopLevelNodelength<-.Communitylength<-.CommunityCollectionlevels<-.Communitylevels<-.CommunityCollectionLinearRegressionByClassLinkageDensityLMablineLoadCollectionLoadCommunityLog10BiomassLog10BLabelLog10CRMRatioLog10MLog10MLabelLog10MNBiomassLog10NLog10NLabelLog10RCMRatioLongestTrophicLevelLongWeightedTrophicLevelLumpNodesLumpTrophicSpeciesMeanMaximumTrophicSimilarityMinimiseSumConsumerGapsMinimiseSumDietGapsnames<-.Communitynames<-.CommunityCollectionNodeNameIndicesNodePropertyNamesNodeQuantitativeDescriptorsNonBasalNodesNonTopLevelNodesNormalisedTrophicGeneralityNormalisedTrophicVulnerabilityNPNPSNumberOfConsumersNumberOfNodesNumberOfNodesByClassNumberOfResourcesNumberOfTrophicLinksNvMConvexHullNvMInterceptNvMInterceptByClassNvMLinearRegressionsNvMSlopeNvMSlopeAndInterceptNvMSlopeAndInterceptByClassNvMSlopeByClassNvMTriTrophicStatisticsNvMTriTrophicTableOmnivoresOmnivoryOrderCollectionOrderCommunityOutDegreePlaceMissingPointsplot.Communityplot.CommunityCollectionPlotAuppervAlowerPlotBCvBRPlotBDistributionPlotBPyramidPlotBRvBCPlotBSpectrumPlotBvMPlotBvRankBPlotCircularWebPlotDegreeDistributionPlotLinearModelsPlotMCvMRPlotMDistributionPlotMRvMCPlotMvBPlotMvNPlotMvRankMPlotNCvNRPlotNDistributionPlotNPSPlotNPSDistributionPlotNPyramidPlotNRvNCPlotNSpectrumPlotNvMPlotNvRankNPlotPredationMatrixPlotRankNPSPlotTLPSPlotWagonWheelPlotWebByLevelPredationMatrixPredationMatrixToLinksPreyAveragedTrophicLevelprint.Communityprint.CommunityCollectionQuantitativeDescriptorsRCMRatioRemoveCannibalisticLinksRemoveIsolatedNodesRemoveNodesResourceLargerThanConsumerResourcesAndConsumersByNodeResourcesByNodeResourcesOfNodesSaveCollectionSaveCommunityShortestPathsShortestTrophicLevelShortWeightedTrophicLevelSiteBySpeciesMatrixsubset.CommunityCollectionSumBiomassByClassSumConsumerGapsSumDietGapssummary.Communitysummary.CommunityCollectionSumMByClassSumNByClassThreeNodeChainsTLPTLPSTopLevelNodesTrophicChainsTrophicChainsStatsTrophicGeneralityTrophicHeightTrophicLevelsTrophicLinkPropertyNamesTrophicLinksForNodesTrophicSimilarityTrophicSpeciesTrophicVulnerability

Dependencies:

A quick introduction to Cheddar
Rendered fromCheddarQuickstart.Rnwusingutils::Sweave

Last update: 2020-02-11
Started: 2013-12-02

Cheddar plots and statistics
Rendered fromPlotsAndStats.Rnwusingutils::Sweave

Last update: 2020-02-11
Started: 2013-12-02

Collections of communities
Rendered fromCollections.Rnwusingutils::Sweave

Last update: 2020-02-11
Started: 2013-12-02

Importing and exporting data in-to and out-of Cheddar
Rendered fromImportExport.Rnwusingutils::Sweave

Last update: 2020-02-11
Started: 2013-12-02

Working with Cheddar communities
Rendered fromCommunity.Rnwusingutils::Sweave

Last update: 2020-02-11
Started: 2013-12-02

Readme and manuals

Help Manual

Help pageTopics
Aggregate communitiesAggregateCommunities AggregateCommunitiesBy
Apply by classApplyByClass SumBiomassByClass SumMByClass SumNByClass
BenguelaBenguela
Body mass, numerical abundance and biomass abundanceBiomass CRMRatio Log10Biomass Log10CRMRatio Log10M Log10MNBiomass Log10N Log10RCMRatio RCMRatio
Body-mass binsBodyMassBins
Broadstone StreamBroadstoneStream
Analysis and visualisation of ecological communitiescheddar-package cheddar
ChesapeakeBayChesapeakeBay
Collection applyCollectionApply
Collection community propertiesCollectionCPS
Collection node propertiesCollectionNPS
Collection trophic-link propertiesCollectionTLPS
Community$<-.Community Community dim<-.Community is.Community length<-.Community levels<-.Community names<-.Community plot.Community print.Community summary.Community [<-.Community [[<-.Community
Community has property?HasM HasN HasTrophicLinks
Collections of communities$<-.CommunityCollection CommunityCollection dim<-.CommunityCollection is.CommunityCollection length<-.CommunityCollection levels<-.CommunityCollection names<-.CommunityCollection plot.CommunityCollection print.CommunityCollection summary.CommunityCollection [.CommunityCollection [<-.CommunityCollection [[<-.CommunityCollection
Names of community propertiesCommunityPropertyNames
Single community propertiesCP
Community propertiesCPS
Node degreeDegree InDegree NormalisedTrophicGenerality NormalisedTrophicVulnerability NumberOfConsumers NumberOfResources OutDegree TrophicGenerality TrophicVulnerability
Node degree distributionDegreeDistribution
Food web IntervalityIntervality MinimiseSumConsumerGaps MinimiseSumDietGaps SumConsumerGaps SumDietGaps
Cannibalistic nodesCannibals FractionCannibalistic IsCannibal
Linear regression by classLinearRegressionByClass
Loading and saving CommunityCollection objectsLoadCollection SaveCollection
Loading and saving Community objectsLoadCommunity SaveCommunity
Lump nodesLumpNodes
Lump trophic speciesLumpTrophicSpecies
MillstreamMillstream
Node connectivityBasalNodes ConnectedNodes FractionBasalNodes FractionConnectedNodes FractionIntermediateNodes FractionIsolatedNodes FractionNonBasalNodes FractionNonConnectedNodes FractionNonTopLevelNodes FractionTopLevelNodes IntermediateNodes IsBasalNode IsConnectedNode IsIntermediateNode IsIsolatedNode IsNonBasalNode IsNonTopLevelNode IsolatedNodes IsTopLevelNode NonBasalNodes NonTopLevelNodes TopLevelNodes
Node name indicesNodeNameIndices
A vector of names of node propertiesNodePropertyNames
Single node propertiesNP
Node propertiesNPS
Number of nodesFractionOfNodesByClass NumberOfNodes NumberOfNodesByClass
Number of trophic linksDirectedConnectance LinkageDensity NumberOfTrophicLinks
NvMConvexHullNvMConvexHull
NvMLinearRegressionsNvMIntercept NvMInterceptByClass NvMLinearRegressions NvMSlope NvMSlopeAndIntercept NvMSlopeAndInterceptByClass NvMSlopeByClass
N-versus-M tri-trophic statisticsNvMTriTrophicStatistics
N-versus-M tri-trophic statisticsNvMTriTrophicTable
OmnivoryFractionOmnivorous IsOmnivore Omnivores Omnivory
Order a collection of communitiesOrderCollection
Order a communityOrderCommunity
pHWebspHWebs
Plot upper-versus-lower link anglesPlotAuppervAlower
Plot circular webPlotCircularWeb
Plot helpersDefaultCategoryColours DefaultCategoryLabelColours DefaultCategorySymbols DefaultLinkColour FormatLM LMabline Log10BLabel Log10MLabel Log10NLabel PlaceMissingPoints PlotLinearModels
Plot node propertiesPlotBvM PlotMvB PlotMvN PlotNPS PlotNvM
Plot distributions of node propertiesPlotBDistribution PlotDegreeDistribution PlotMDistribution PlotNDistribution PlotNPSDistribution
Plot rank of node propertiesPlotBvRankB PlotMvRankM PlotNvRankN PlotRankNPS
Plot trophic-link propertiesPlotBCvBR PlotBRvBC PlotMCvMR PlotMRvMC PlotNCvNR PlotNRvNC PlotPredationMatrix PlotTLPS
Plot wagon wheelPlotWagonWheel
Plot web by levelPlotWebByLevel
Predation matrixPredationMatrix
Predation matrix to trophic linksPredationMatrixToLinks
Pyramid plotsPlotBPyramid PlotNPyramid
Quantitative descriptorsNodeQuantitativeDescriptors QuantitativeDescriptors
Remove cannibalistic trophic linksRemoveCannibalisticLinks
Remove isolated nodesRemoveIsolatedNodes
Remove nodesRemoveNodes
Resource larger than consumerResourceLargerThanConsumer
Resources and consumers of nodesConsumersByNode ConsumersOfNodes ResourcesAndConsumersByNode ResourcesByNode ResourcesOfNodes TrophicLinksForNodes
Path lengthsCharacteristicPathLength ShortestPaths
Community collection site by species matrixSiteBySpeciesMatrix
SkipwithPondSkipwithPond
Spectrum plotsPlotBSpectrum PlotNSpectrum
A subset of a collection of communitiessubset.CommunityCollection
Three-node chainsThreeNodeChains
Tuesday Lake datasetsTL84 TL86
A single trophic-link propertyTLP
Trophic-link propertiesTLPS
Trophic chainsTrophicChains
Trophic chains statisticsTrophicChainsStats
Trophic levelsChainAveragedTrophicLevel FlowBasedTrophicLevel LongestTrophicLevel LongWeightedTrophicLevel PreyAveragedTrophicLevel ShortestTrophicLevel ShortWeightedTrophicLevel TrophicHeight TrophicLevels
Trophic link property namesTrophicLinkPropertyNames
Trophic similarityMeanMaximumTrophicSimilarity TrophicSimilarity
Trophic speciesTrophicSpecies
Ythan EstuaryYthanEstuary